Protein Physics

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Protein Physics

• A. V. Finkelstein
• O. B. Ptitsyn
• LECTURE 13
• www.nd.edu/aasztalo

Andrea Asztalos, 2007 September 26
porin
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One Classification of Proteins
1.Fibrous Proteins

• mostly structural proteins
• an elongated, unidimensional structure

2.Membrane Proteins

• reside within the cellular intracellular
  membrane
• transport molecules in and out of the cell

3.Globular Proteins

• short chains packed into a compact 25-40Å
  globule
• closely folded structure
• water soluble proteins
• Ex egg albumin, hemoglobin, many enzymes

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Globular Proteins Domains

• Short chains packed into a globule
• as tightly as organic molecules
• in a crystal.

• Domain sizes 20 -692, average 100 residues
• Each of them folds individually
• Contain a hydrophobic core built from sheets
• and helices connected by loop regions.

?-crystallin
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Structural Classes of Globular Proteins/Domains
Further Simplified Models of Protein Structures
Architecture of protein
Topology of protein
Packing
Fold
Folding Pattern
Level of Simplification
Usefulness classification and outlining their
typical features
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ß-proteins

• Mostly antiparallel arrangement

• Two sheets packed against each other

• Basic packing types

Top views
Orthogonal Packing
Aligned Packing
Bottom views
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ß-barrel/cylinder
Retinol-binding protein
Porin
ß-hairpin
ß-hairpin
Meander (up down) motif
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Acid protease
Serine protease
Topology Diagrams
Overlapping loop uncommon
Greek key
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ß-proteins
So far

• Packing types orthogonal aligned
• Structural architectures
• ß-barrel
• Motifs present in structural architectures
• (super-secondary structures) ß-hairpin,
  meander, greek key

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ß-sandwich
Greek key 2 - 5 Greek key 3 - 6
Bottom view N-end ? C-end
complete Greek key
Immunoglobulin ?
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ß catabolite activating protein
?-crystallin
virus coat protein
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Greek key Jelly roll
Greek key
Jelly roll
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ß-proteins
So far

• Packing types orthogonal aligned
• Structural architectures
• ß-barrel, ß-sandwich
• Motifs present in structural architectures
• (super-secondary structures) ß-hairpin,
  meander, greek key, jelly roll

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ß-propeller
multi-blade (4/5/6/7/8) propeller three
ß-sandwiches
Neuraminidase
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ß-prism(helix)

• Formed by three parallel (unusual) beta-sheets

Acyl-transferase (left-handed helix) uncommon
Pectate lyase (right-handed helix) common
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Possible topologies composed of four ß-strands
Efimovs abcd structures
Spatial structures with the same Greek key
topology
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ß-proteins

• Built up from mostly antiparallel ß-strands
  (based on ß-hairpins)
• Packing types orthogonal aligned
• Structural architectures
• ß-barrel, ß-sandwich, ß-propeller, ß-prism
• Motifs present in structural architectures
• (super-secondary structures)
• ß-hairpin, meander, greek key, jelly roll,